Separate Enrollment and Line Item Veto Act of 1999

Separate Enrollment and Line Item Veto Act of 1999 - Prohibits the Committee on Appropriations of either the House of Representatives or the Senate from reporting an appropriation measure that fails to contain such level of detail on the allocation of an item of appropriation proposed by that House as is set forth in the accompanying committee report.

Prohibits a congressional committee from reporting an authorization measure containing new direct spending or new tax benefits unless such measure presents such items separately and the accompanying committee report contains the necessary level of detail.

Prohibits the filing of conference reports on appropriations measures that fail to contain such level of detail on the allocation of an item as is set forth in the accompanying statement of managers.

(Sec. 3) Allows the waiver or appeal of such prohibitions by a three-fifths vote of the appropriate House.

(Sec. 4) Requires separate enrollment of each item of appropriation or authorization in measures passed by both Houses in identical form. Provides for congressional consideration of such bills.

(Sec. 6) Provides for expedited judicial review of provisions of this Act in the U.S. District Court for the District of Columbia and direct appeals to the Supreme Court.

(Sec. 7) Amends the Balanced Budget and Emergency Deficit Control Act of 1985 (Gramm-Rudman-Hollings Act) and the Congressional Budget Act of 1974 to prohibit the inclusion of non-emergency spending proposals in emergency spending legislation. Allows such proposals to contain rescissions of budget authority or provisions that reduce direct spending.

(Sec. 8) Requires savings from rescissions bills to be used for deficit reduction.

(Sec. 9) Requires the President to submit legislation for the periodic review, reauthorization, and sunset of tax expenditures with the FY 2000 budget.

Requires the inclusion in the budget beginning with FY 2002 of a performance plan for measuring the overall effectiveness of tax expenditures, including a schedule for periodically assessing the effects of specific tax expenditures in achieving performance goals.

Directs the Director of the Office of Management and Budget to include as a pilot project the periodic analyses of such goals and the relationship between tax expenditures and spending programs.

Amends the Congressional Budget Act of 1974 to prohibit consideration in the House and the Senate of legislation that contains a tax expenditure unless the expenditure terminates not later than ten years after the date of its enactment.

(Sec. 11) Makes this Act effective until the end of FY 2004.